MATLAB: Converting Hashtables with Matlab

javaMATLABmatlab java microscopy bioinformatics

Hey everyone,

So, I have these files generated in a format called .c01 (By Cellomics). I downloaded a App Package from this website https://www.openmicroscopy.org/site/support/bio-formats5.2/developers/matlab-dev.html which converts the .c01 file into a cell structure. I think all the raw data is stored in the 'Hashtable' cell. So I've extracted that cell and get an Object – 1×1 Hashtable. I have zero experience with Java and i'm having a heck of a time figuring out how to convert this hash table into an array of raw data values. Is there anyone with any experience with this that can help?

Best Answer

Hopefully this example helps to explain. You can obviously skip over the creating bit as you already have a table and presumably you just want to get all of the values out of it.

% create example Java hashtable and add some key/value pairs
h = java.util.Hashtable;
h.put('Name', 'John');
h.put('Country', 'UK');
% retrieve the value for a specific key
h.get('Name');
% retrieve all key names
allKeys = arrayfun(@char, h.keySet.toArray, 'UniformOutput', false);
% retrieve all key values
allValues = cellfun(@(x) h.get(x), allKeys, 'UniformOutput', false);

Related Solutions

MATLAB: Are cell arrays converted to arrays of type java.lang.Object, rather than to a particular type, in MATLAB 7.2 (R2006a)

This is an error within the documentation for MATLAB 7.2 (R2006a) within the Calling Java from MATLAB section of the External Interfaces manual.

The documentation should read as follows:

"MATLAB automatically converts the cell array elements to java.lang.Object class objects. Note that in order for a cell array to be passed from MATLAB, the corresponding argument in the Java method signature must specify java.lang.Object or an array of java.lang.Object."

To pass an array to java, you can either manually create an array of objects of the correct type, or modify the Java method to accept arguments of type java.lang.Object.

1. For example to create a Java array of the appropriate type do the following:

jHarray = javaArray('java.util.Hashtable',4);
jHarray(1) = java.util.Hashtable;
jHarray(1).put('a',3);
jHarray(2) = java.util.Hashtable;
jHarray(2).put('a',12);
jHarray(3) = java.util.Hashtable;
jHarray(3).put('a',24);
jHarray(4) = java.util.Hashtable;
jHarray(4).put('a',36);
MatlabJavaBug.hello(jHarray);

2. Alternatively, you can convert the method to have the following signature. Before using the elements of the array, you will need to cast them to the appropriate class. For example the function header would be modified as follows:

 public static void hello(java.lang.Object hash[])

MATLAB: How to merge a cell 2×60 into 1×60

One possible way:

newcellarray = cellfun(@(column) cell2mat(column), num2cell(yourcellarray, 1), 'UniformOutput', false);

Best Answer

Related Solutions

MATLAB: Are cell arrays converted to arrays of type java.lang.Object, rather than to a particular type, in MATLAB 7.2 (R2006a)

MATLAB: How to merge a cell 2×60 into 1×60

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